ABSTRACT
Objective:To explore the role of a disintegrin-like and metalloproteinase with throm bospondin typeⅠmotifs-8(ADAMTS8) gene in lung adenocarcinoma and its mechanism.Methods:Selected lung adenocarcinoma data sets GSE75037 and GSE116959 and lung adenocarcinoma transcriptome data and clinical information from the TCGA database; useed R software to analyze differential genes in lung adenocarcinoma tissues, and performed GO enrichment analysis and KEGG signal pathway enrichment for differential genes set analysis; analyzed the expression of ADAMTS8 gene in lung adenocarcinoma and its correlation with patient survival and prognosis; CCK-8 experiment detects the effect of ADAMTS8 overexpression or knockdown on the proliferation of A549 cells; Western blot detected ADAMTS8 overexpression or knockdown effect on Wnt/β-catenin signaling pathway. Results:The combined analysis found that 395 genes were up-regulated in lung adenocarcinoma samples, and 716 genes were down-regulated; ADAMTS8 was under-expressed in lung adenocarcinoma tissues, and its expression level was related to tumor stage; low-expression of ADAMTS8 was associated with shorter survival time, poor prognosis, Cox regression analysis showed that ADAMTS8 can be used as an independent prognostic marker for patients with lung adenocarcinoma; CCK-8 results showed that overexpression of ADAMTS8 can inhibit the proliferation of A549 cells, knocking down ADAMTS8 can promote the proliferation of A549 cells ( P<0.05); Western blot results showed that after overexpression of ADAMTS8, the protein levels of β-catenin, cyclin D1 and c-Myc in cells were significantly reduced ( P<0.05), while knocking down ADAMTS8 could cause the protein levels of β-catenin, cyclin D1 and c-Myc in cells increased significantly ( P<0.05). Conclusions:ADAMTS8 is under-expressed in lung adenocarcinoma and can be used as an independent prognostic marker for patients. Overexpression of ADAMTS8 may inhibit the proliferation of lung adenocarcinoma cells by inhibiting the activity of Wnt/β-catenin signaling pathway.
ABSTRACT
The expression, function and prognostic significance of epoxide hydrolase 2 (EPHX2) in hepatocellular carcinoma (HCC) were comprehensively analyzed through collecting HCC tissues and public database. The GEO and MitoCarta databases were used to identify the mitochondria-related differentially expressed genes (DEGs) in HCC. The Cancer Genome Atlas (TCGA) database was applied to analyze the expression levels of DEGs in HCC, including EPHX2 and its co-expressed genes. The R package was applied to draw the Kaplan-Meier survival curve and gene function enrichment analysis. The STRING database and GSEA software were used to analyze the protein-protein interaction (PPI) network and gene set enrichment analysis. qPCR and GEO database were applied to verify the expression level of EPHX2 in HCC. In the present study, a total of 15 mitochondria-related DEGs were identified in HCC. The expression of EPHX2 in HCC was significantly decreased compared to the normal liver tissues (P < 0. 01). The expression of EPHX2 was related to gender, tumor stage and grade in HCC, but not associated with age, T stage, et al in HCC. Moreover, compared with the patients with lower expression of EPHX2, patients with higher expression of EPHX2 had a better prognosis. EPHX2 was associated with fatty acid degradation. In addition, PPI results indicated that HAO1, AGXT, ACOX1, GSTκ1, SCP-2, CAT, CYP2C8, CYP2C9, CYP2B6, and CYP2J2 were co-expressed with EPXH2 in HCC. Furthermore, GSEA results showed that the group with lower expression of EPHX2 was positively correlated with the gene set of liver cancer cell proliferation and liver cancer recurrence. qPCR and GEO database results verified that the expression of EPHX2 was significantly decreased in HCC. The expression of EPHX2 was decreased in HCC, strongly suggesting that EPHX2 might function as a tumor suppressor gene in HCC. However, the potential mechanism of EPHX2 in HCC needs to be further verified.
ABSTRACT
OBJECTIVE: To explore the related signaling pathways, biomarkers and prognostic genes of malignant pleural mesothelioma(MPM) based on the gene chip and second-generation sequencing datasets in public database by bioinformatics-related method. METHODS: MPM microarray expression datasets GSE51024 and GSE2549, with 82 and 49 MPM patients, respectively, were downloaded from the Gene Expression Omnibus database. The RNA sequencing data of 86 MPM patients were downloaded from the The Cancer Genome Atlas(TCGA). The weighted gene co-expression network analysis(WGCNA) and differentially expressed genes(DEGs) screening were used to screen and identify hub genes in the GSE51024 dataset by RStudio 4.0 software. The gene set enrichment analysis(GSEA) was used to explore relevant signaling pathways. Finally, a total of 135 MPM gene expression data from GSE2549 dataset and TCGA database were used to verify the hub genes. RESULTS: The green key gene module identified by the WGCNA was highly correlated with MPM, with a correlation coefficient of 0.83(P<0.01). A total of 3 245 DEGs were screened by DEGs analysis. Among them, 1 229 genes were up-regulated and 2 016 genes were down-regulated. GSEA results showed that the genes were significantly enriched in the areas of G2/M cell cycle checkpoint, epithelial-mesenchymal transition, E2 F target gene, and mitotic spindle pathways. Three hub genes were screened, including the proliferating cell nuclear antigen-associated factor(PCLAF), nucleolar and spindle-associated protein 1(NUSAP1) and topoisomerase Ⅱ-α(TOP2 A). Compared with para-cancerous tissues, normal pleural tissues or lung tissues, the relative expression of PCLAF, NUSAP1 and TOP2 A were increased in the MPM tissues(all P<0.05). Downregulation of these three genes was correlated with good prognosis, and upregulation of these three genes was correlated with poor prognosis in the patients. CONCLUSION: G2/M checkpoint, epithelial-mesenchymal transition, E2 F target gene and mitotic spindle pathway are the key signaling pathways in the occurrence and development of MPM. PCLAF, TOP2 A and NUSAP1 genes could be the biomarkers for the prognosis of MPM.
ABSTRACT
We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.